Molecular characterization of a mitochondrial DNA segment from the Japanese scallop (Patinopecten yessoensis): Demonstration of a region showing sequence polymorphism in the population

A 1.3-kb mitochondrial DNA segment from the Japanese scallop Patinopecten y essoensis was cloned and sequenced. This segment contained the transfer RNA (Met) gene and partial sequences of 2 ribosomal RNA genes, together with 2 separate noncoding regions (designated NcR1 and NcR2). The NcR regions deri ved from 78 individuals cultured in Lake Saroma or Matsu Bay, were sequence d, and we found 15 loci with sequence alterations including 13 substitution s, I deletion, and I insertion (I locus in NcR1, 14 loci in NcR2), and 17 h aplotypes. Of the 17 haplotypes, 10 were found in the Saroma population onl y, 3 in the Mutsu Population only, and 4 in both populations. The gene dive rsity and nucleotide diversity values were, respectively, 0.87 and 0.0069 f or the Saroma population, 0.63 and 0.0040 for the Mutsu population, and 0.8 3 and 0.0203 overall. Thus the NcR segment was considered to have sufficien t sequence variation for population genetic studies. The 16 variants of the NcR2 sequence were separated successfully by denaturing gradient gel elect rophoresis, confirming the sequence variation in NcR2.